Piezoelectric stack, such as Aluminum nitride (AlN) based piezoelectric stack, has gained popularity in recent years as a trend for next generation Microelectromechanical Systems (MEMS), including Piezoelectric Micromachined Ultrasonic Transducers (PMUT), inertial sensor, resonator, radio frequency (RF) filter, etc. Multi-layer AlN provides for good diaphragm/cantilever flatness control and offers more signal output. However, there is a need for a process that allows structures to be formed on the multi-layer piezoelectric stack without damaging the interface between the piezoelectric layers